Biology subjects

Venkatesh, K. V.

Publications and source records attributed to Venkatesh, K. V..

4 recordsLinked to original sources

bioRxiv2020

Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Complex regulatory interactions between genetic and metabolic networks together confer robustness against external and internal perturbations in an organism such as Escherichia coli. In balanced exponential growth, this robustness is attributed to cost-effective metabolism by means of efficient resource allocation coordinated by the interplay of global transcriptional regulators with growth-rate dependent machinery. Here, we reappraise the role of global transcriptional regulators FNR, ArcA and IHF, integral to sustaining proteome-efficiency in anaerobic fermentative conditions, fundamental for optimal growth of E. coli. We reveal at the transcriptome and metabolome level, that absence of these global regulators ensued a disruption of nitrogen homeostasis, overexpression of otherwise unnecessary or hedging genes and impairment in core bottleneck steps and amino acid metabolism. Notably, our findings emphasize their importance in optimizing the metabolic proteome resources essential for rapid exponential growth. Consequentially, the perturbations in the metabolic proteome as a result of deletion of global regulators unbalances the ribosomal proteome share imposing a high translation program, though at the expense of lowered efficiency. We illustrate that disruption of this inherent trade-off between metabolic and ribosomal proteomic investment eventually culminate to lowered growth rates. Despite no changes in gene expression related to glucose import, our findings elucidate that the accumulations of intracellular metabolites directly modulated by growth rate, negatively impacts the glucose uptake. Our results employing the proteome allocation theory and quantitative experimental measurements, suffices to explain the physiological consequences of altered translational and metabolic efficiency in the cell, driven by the loss of these global regulators.

systems biology↗

bioRxiv2020

Elucidating the regulatory role of CRP in coordinating protein biosynthesis machinery with metabolism that defines growth optimality in Escherichia coli

Evolution entails the orchestration of cellular resources together with mutations to achieve fitter phenotypes. Here, we determined the system-wide pleiotropic effects that redress the significant perturbations caused by the deletion of global transcriptional regulator CRP in Escherichia coli when evolved in the presence of glucose. We elucidated that absence of CRP results in alterations in key metabolic pathways instrumental for the precise functioning of protein biosynthesis machinery that subsequently corroborated with intracellular metabolite profiles. Apart from acquiring mutations in the promoter of glucose transporter ptsG, the evolved populations recovered the metabolic pathways to their pre-perturbed state with amelioration of protein biosynthesis machinery coupled with fine-tuned proteome re-allocation that enabled growth recovery. However, ineffective utilization of carbon towards biomass as perceived from ATP maintenance flux and costly amino acid accumulations poses a limitation. Overall, we comprehensively illustrate the genetic and metabolic adjustments underlying adaptive evolvability, fundamental for understanding the growth physiology.

systems biology↗

bioRxiv2020

Ligand Sensing Enhances Bacterial Flagellar Motor Output via Stator Recruitment

The phenomenon of chemotaxis in bacteria, where the cells migrate towards or away from chemicals, has been extensively studied in the past. For flagellated bacteria such as Escherichia coli, a change in chemical concentration in its environment is sensed by a chemoreceptor and communicated via a well-characterised signalling pathway to the flagellar motor. It has been widely accepted that the signals change the rotation bias of the motor without influencing the motor speed. Here, we present results to the contrary and show that the bacteria is also capable of modulating motor speed on merely sensing a ligand. Step changes in concentration of non-metabolisable ligand cause temporary recruitment of stators leading to a momentary increase in motor speeds. For metabolisable ligand, the combined effect of sensing and metabolism leads to higher motor speeds for longer durations. Swimming speeds measured at the population level corroborate the observations. Experiments performed with mutant strains delineate the role of metabolism and sensing in the modulation of motor speed and show how speed changes along with changes in bias can significantly enhance bacterias response to changes in its environment.

biophysics↗

bioRxiv2019

\"Viscotaxis\" - Directed Migration of Mesenchymal Stem Cells in Response to Loss Modulus Gradient

Directed cell migration in response to chemical and mechanical gradients plays a crucial role in physiological and pathological conditions. One such mechanical cues that is known to influences cell migration is the gradient of substrate elastic modulus (E). However, the elastic modulus alone cannot fully define the material properties of the cellular microenvironment, which often has both elastic and viscous characteristics. In this study, we investigated the influence of the gradient of viscous nature, as defined by loss modulus, G\", on cell migration. We cultured human mesenchymal stem cells (hMSCs) on a collagen-coated polyacrylamide gel with constant elastic property, as defined by the storage modulus G, but with the gradient of loss modulus G\". We found hMSCs to migrate from high to low loss modulus. We have termed this, thus far unreported, directional cellular migration as \"Viscotaxis\". We have confirmed uniform collagen density and constant storage modulus of the gel by fluorescence microscopy and atomic force microscopy to eliminate the possibilities of haptotaxis and durotaxis. We hypothesize that material creep in the high loss modulus region hinders the building up of the cellular traction, leading to a force asymmetry that drives the observed viscotaxis. To verify our hypothesis, we estimated the cellular traction on gels with high and low loss moduli. We indeed found that cells apply higher traction force on more elastic materials i.e. materials with low loss modulus. On the disruption of actomyosin contractility with myosin inhibitor blebbistatin and ROCK inhibitor Y27632, directional migration was lost. Further, we showed that cells can maintain a stable morphology on a low loss modulus substrate but due to its inability to build up stable cellular traction on a substrate with high loss modulus, the cell spreading remains in a dynamic state. Our findings in this paper highlight the importance of considering the viscous modulus while preparing stiffness-based substrates for the field of tissue engineering.

biophysics↗